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#include "PDBReader.hpp" |
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#include "RigidBody.hpp" |
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#include "GridBuilder.hpp" |
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#include "SphereHarm.hpp" |
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#define MK_STR(s) # s |
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#define STR_DEFINE(t, s) t = MK_STR(s) |
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vector<double> sigmaGrid; |
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vector<double> epsGrid; |
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vector<double> sGrid; |
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SphereHarm* harmonize; |
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double mass, rpar, eps; |
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double xyz3[3]; |
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double moments[3][3]; |
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string fileName; |
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char vdwFileName[2002]; |
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char structureFileName[2002]; |
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char temp[200]; |
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char readLine[500]; |
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char xyzFile[200]; |
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char shapeFile[200]; |
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char shapeName[80]; |
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FILE *vdwFile, *structureFile; |
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char* ffPath_env = "VDW_PATH"; |
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char* ffPath; |
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int nTokens; |
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int FF; |
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int bandwidth; |
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int gridwidth; |
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short int gotMatch; |
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//parse the command line options |
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strcpy(xyzFile, file); |
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token = strtok(xyzFile, period); |
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strcpy(xyzFile, token); |
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strcat(xyzFile, "ref.xyz"); |
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strcpy(shapeFile, token); |
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strcpy(shapeName, token); |
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> |
strcat(xyzFile, "Ref.xyz"); |
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strcat(shapeFile, ".shape"); |
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strcat(shapeName, "_RB_0"); |
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ofstream xfiles(xyzFile); |
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//the bandwidth has a default value (default=16), so it is always given |
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bandwidth = args_info.bandwidth_arg; |
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gridwidth = bandwidth*2; |
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|
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if (args_info.charmm_given) { |
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FF=CHARMM; |
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xfiles << rb->getNumAtoms() << "\n\n"; |
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for (k=0; k<rb->getNumAtoms(); k++){ |
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rb->getAtomRefCoor(xyz3, k); |
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< |
xfiles << rb->getAtomType(k) << "\t" << |
| 275 |
> |
xfiles << rb->getAtomBase(k) << "\t" << |
| 276 |
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xyz3[0] << "\t" << xyz3[1] << "\t" << |
| 277 |
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xyz3[2] << "\n"; |
| 278 |
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} |
| 279 |
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|
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< |
gb = new GridBuilder(rb, bandwidth*2); |
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> |
gb = new GridBuilder(rb, gridwidth); |
| 281 |
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| 282 |
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cout << "Doing GridBuilder calculations...\n"; |
| 283 |
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gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 284 |
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< |
//write out the grid files |
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gb->printGridFiles(); |
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> |
|
| 287 |
> |
//load the grid element values to the main grid vectors |
| 288 |
> |
for (k=0; k<gridwidth*gridwidth; k++){ |
| 289 |
> |
sigmaGrid.push_back(gb->passSig(k)); |
| 290 |
> |
sGrid.push_back(gb->passS(k)); |
| 291 |
> |
epsGrid.push_back(gb->passEps(k)); |
| 292 |
> |
} |
| 293 |
> |
|
| 294 |
> |
//build the spherical harmonic transform object |
| 295 |
> |
harmonize = new SphereHarm( bandwidth ); |
| 296 |
> |
rb->getI(moments); |
| 297 |
> |
harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(), |
| 298 |
> |
moments); |
| 299 |
> |
|
| 300 |
> |
//do the transforms and write to the shapes file |
| 301 |
> |
harmonize->doTransforms(sigmaGrid); |
| 302 |
> |
harmonize->printToShapesFile(shapeFile, 0); |
| 303 |
> |
harmonize->doTransforms(sGrid); |
| 304 |
> |
harmonize->printToShapesFile(shapeFile, 1); |
| 305 |
> |
harmonize->doTransforms(epsGrid); |
| 306 |
> |
harmonize->printToShapesFile(shapeFile, 2); |
| 307 |
> |
|
| 308 |
> |
//clean everything up |
| 309 |
> |
harmonize->~SphereHarm(); |
| 310 |
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} |
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|
| 312 |
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int count_tokens(char *line, char *delimiters) { |
